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Consider the roots: examining barley belowground in the search for adaptation
(Montana State University - Bozeman, College of Agriculture, 2024) Williams, Jessica Lynn; Chairperson, Graduate Committee: Jamie Sherman; This is a manuscript style paper that includes co-authored chapters.
Barley is important for global food security and sustaining the economically valuable malt industry. Montana is a top barley producer in the United States, but terminal drought stress poses a significant threat to this production by negatively impacting yield and quality. New crop varieties with enhanced environmental adaptation and soil resource extraction would help address this and other issues facing modern agriculture. Stay-green is a trait that extends grain fill in cereals and can stabilize yield and quality under drought. However, this trait and its benefits can be inconsistent across environments and its successful incorporation into breeding strategies would benefit from expanded understanding of stay-green. Roots may play a role in stay-green physiology. Roots provide plants with the water and nutrients needed for growth and are important for crop performance in their own right. Different root system architectures provide adaptation to different environmental stressors, but studying these belowground structures is challenging. Adaptation is also impacted by soil properties and microbial communities. For this dissertation, roots were examined in greenhouse seedling assays and field trials in Montana. Agronomic performance was also assessed for malt barley and spring wheat cultivars varying for stay-green, a biparental barley population segregating for stay-green, and a diverse mapping population of barley lines from different breeding programs. Stay-green cultivars had a greater percentage of deep roots, more prolonged root growth during grain fill, and greater yield. Analysis of the biparental population identified genetic co-segregations of stay-green, root phenotypes, grain quality, and quality stability between environments, further supporting the benefit of stay-green in dry environments and its connection to roots. The diverse mapping population was used to find associations between the relative abundances of bacteria in the rhizosphere and barley genetic loci, that were mostly environment specific. Rhizospheric bacteria may be involved in local adaptation of plants. Finding plant genetic signal for these microbial characteristics supports the idea that it may be possible to breed crops with enhanced ability to recruit beneficial microbiomes if environmental influence and agronomic impact can be understood. Root examination remains a challenging but worthwhile avenue to pursue in crop adaptation research.
Leveraging a global spring, 2-row barley population to accelerate the development of superior forage barley varieties for Montana growers
(Montana State University - Bozeman, College of Agriculture, 2021) Hoogland, Traci Janelle; Chairperson, Graduate Committee: Jamie Sherman
As more people around the globe escape poverty, they are eating more meat and dairy products. To support this increased demand for animal products there is an urgent need to develop more sustainable high-quality forage and hay crops for the livestock production industry. Barley (Hordeum vulgare spp. vulgare L.) is considered one of the most drought tolerant of the annual cereals and spring barley has been shown to out yield established perennial forages under drought conditions in central Montana (Cash, Surber, & Wichman, 2006). To accelerate the development of superior forage barley varieties for Montana, the following goals were identified 1) Utilize a genome wide association analysis to find genetic regions related to key forage and agronomic traits, 2) Use statistical modeling to a) examine the relationship between difficult to measure forage traits such as quality and yield, and easy to measure agronomic traits such as flowering time and plant height, b) identify agronomic traits that can be used as proxies for yield and quality in the earliest stages of the breeding program when genetic and phenotypic variability are at their greatest. Through these techniques the importance of variation in timing of plant maturity was identified. Statistical modeling showed that variability in forage yield and quality was observed to be closely related to variability in the timing of heading and soft-dough dates. Plant height was also determined to be of importance especially for biomass yield. Through genome-wide association analysis, novel QTL were discovered in relation to all studied traits. QTL were detected on all seven chromosomes and the majority of forage trait QTL co-located with QTL related to the timing and progression of plant development and maturity. This appeared to indicate that in a population of global barley accessions, the loci with the greatest impact on forage traits may be those containing genes regulating plant development and senescence. This further strengthened the evidence from the modeling study that a relationship exists between the two trait categories: traits for measuring the timing of plant development and forage traits.
Genetics of seed dormancy in wheat and barley
(Montana State University - Bozeman, College of Agriculture, 2020) Vetch, Justin Michael; Chairperson, Graduate Committee: Michael J. Giroux; Robert N. Stougaard, John M. Martin and Michael J. Giroux were co-authors of the article, 'Revealing the genetic mechanisms of preharvest sprouting' in the journal 'Plant science' which is contained within this dissertation.; Robert N. Stougaard, John M. Martin and Michael J. Giroux were co-authors of the article, 'Allelic impacts of TaPHS1, TaMKK3, and Vp1B3 on preharvest sprouting of northern Great Plains winter wheats' in the journal 'Crop science' which is contained within this dissertation.; Jason G. Walling, Jamie D. Sherman, John M. Martin and Michael J. Giroux were co-authors of the article, 'Mutations in the HvMKK3 AND HvAlaAT1 genes affect barley pre-harvest sprouting and after-ripened seed dormancy' in the journal 'Crop science' which is contained within this dissertation.; Philip L. Bruckner, John M. Martin and Michael J. Giroux were co-authors of the article, 'TAMFT homeologs are associated with preharvest sprouting winter wheat' submitted to the journal ''Crop science' which is contained within this dissertation.
Montana producers have many biotic and abiotic stresses to contend with. One of interest to avoid is preharvest sprouting (PHS), which is the precocious germination of grains before harvest. PHS affected grain is discounted at the elevator, resulting in grain being unsuitable for many foods and direct losses to producers. PHS is not widespread every year in Montana but in some years causes large economic loss. Although PHS is a response to environmental cues it is largely controlled by genetics. Genes that control seed dormancy are the most likely candidate genes for PHS resistance and the series of studies presented in this dissertation examine the impact of several genes upon small grain PHS susceptibility. The studies used several methods to assess PHS susceptibility and determine which alleles of individual genes were present. The methods included seed dormancy screening assays, alpha amylase enzyme activity analysis, falling numbers analysis, genotyping by direct sequencing and via use of various markers, RNA-sequencing, and gene expression analysis. The first study served as a PHS susceptibility survey and provides PHS tolerance information on MT grown wheat varieties. This study also found that of the three most reported PHS associated genes (TaMFT 3A, TaMKK3 4A, and TaVp1 3B), only TaMFT 3A was associated with PHS in Montana winter wheats, even though the previously reported variation was observed in all three genes. The second study looked at PHS susceptibility among current and historically grown barley varieties. It was found that malt varieties vary greatly in their susceptibility to PHS with the top grown AMBA recommended varieties among the most susceptible. It was also found that a previously unstudied mutation in the HvMKK3 gene is associated with PHS susceptibility. Interestingly, HvMKK3 and HvAlaAT1 affect dormancy at different time points in grain maturity indicating dormancy may be tailored to a specific timeframe (high dormancy at harvest with rapid decay of dormancy after harvest). The final study revisited winter wheat PHS and found that the TaMFT 3B and 3D homeologs are associated with PHS which has not been shown to date.
Improving malt barley agronomics via allelic selection of senescence and flowering time controlling genes
(Montana State University - Bozeman, College of Agriculture, 2020) Alptekin, Burcu; Chairperson, Graduate Committee: Andreas M. Fischer; Dylan Mangel, Duke Pauli, Tom Blake, Jennifer Lachowiec, Traci Hoogland, Andreas Fischer and Jamie Sherman were co-authors of the article, 'Combined effects of glycine-rich RNA binding protein and a NAC transcription factor extend grain fill duration and improve malt barley agronomic performance' submitted to the journal 'Theoretical and applied genetics' which is contained within this thesis.; Dylan Mangel, Duke Pauli, Tom Blake, Jennifer Lachowiec, Jamie Sherman and Andreas Fischer were co-authors of the article, 'Dissecting the effects of senescence-regulating HvNAM1 and HvNAM2 transcription factors on malt barley agronomics' submitted to the journal 'Molecular breeding' which is contained within this thesis.; Dylan Mangel, Duke Pauli, Tom Blake, Hannah Turner, Jennifer Lachowiec, Jamie Sherman and Andreas Fischer were co-authors of the article, 'Allelic selection of senescence and flowering time controlling genes confers malt extract stability' submitted to the journal 'Journal of the American Society of Brewing Chemists' which is contained within this thesis.
Malt barley (Hordeum vulgare L.) is a high-profit crop for farmers; yet, its production raises challenges that need to be addressed. The standards for grain quality in malt barley are stringent, and the rejection of non-qualified grains by maltsters is the leading cause of revenue loss for malt barley producers. Rejection is mainly due to high grain protein content and low kernel plumpness which both cause significant problems in the malting process. While proper growing practices can improve malt quality, the industry requires genotypes that have more stable malt quality. Therefore, understanding the molecular mechanisms associated with grain quality can be applied to improve selection of superior malt varieties. A considerable volume of literature has suggested that regulation of whole-plant senescence and flowering processes in cereals have direct influences on grain yield and quality parameters. The central question in this dissertation examined whether malt barley agronomic and end use quality can be improved by the selection of varying alleles for genes associated with plant development. With this purpose, two whole-plant senescence-regulating NAM, ATAF and CUC (NAC) transcription factors, HvNAM1 and HvNAM2, and a flowering-time controlling Glycine-Rich RNA Binding Protein (HvGR-RBP1) were studied. Molecular markers for selection of alleles from varieties 'Karl' (with consistently low grain protein) and 'Lewis' were developed, and an advanced-generation malt barley breeding population was genotyped. Statistical analysis of growth parameters from this population showed that selection of HvNAM1 'Karl', HvNAM2 'Karl' and HvGR-RBP1 'Lewis' alleles ensures a longer grain filling period in malt barley. Plants with prolonged grain filling also exhibited increased kernel plumpness and test weight. Additionally, selection of 'Karl' alleles for both NAC genes decreased grain protein content ensuring grain quality for malting. The improvement of grain characteristics correlated with improved malt phenotypes, for example a ~2% increase in malt extract, and improvement in other malt characteristics such as beta-glucan content and alpha-amylase activity was observed. Overall, these data show that molecular genetics and allelic selection for genes controlling plant development is promising for advancing malt quality. Research performed here has a direct potential for improving the profits for malt barley producers.
Evaluation of wheat production practices under wheat streak mosaic disease risk and wheat stem sawfly pressure in Montana
(Montana State University - Bozeman, College of Agriculture, 2020) McKelvy, Uta; Chairperson, Graduate Committee: Mary Burrows; Monica Brelsford, Jamie Sherman and Mary Burrows were co-authors of the article, 'Susceptibility and tolerance of winter wheat, spring wheat and barley cultivars to mechanical inoculation with wheat streak mosaic virus' submitted to the journal 'Plant health progress' which is contained within this dissertation.; Peggy Lamb, Monica Brelsford and Mary Burrows were co-authors of the article, 'Impact of planting date, seeding rate and cultivar choice on spring and winter wheat productivity and profitability in Montana' submitted to the journal 'Agronomy journal' which is contained within this dissertation.; David Weaver and Mary Burrows were co-authors of the article, 'Evaluation of chemical and cultural management practices for wheat stem sawfly control and effects on beneficial insects in spring wheat in Montana' submitted to the journal 'Journal of economic entomology' which is contained within this dissertation.
Wheat (Triticum aestivum L.) is an economically important crop for Montana's agricultural industry. Wheat streak mosaic (WSM) is an important viral disease in Montana and the wheat stem sawfly (WSS; Cephus cinctus Norton) is a major insect pest in the state. Understanding these disease and pest problems and the factors that promote and suppress disease and pest pressure forms the foundation for a successful integrated pest management program. In this dissertation, we evaluate wheat production practices in Montana and provide information on the effectiveness and implications of cultural and chemical management practices in mitigating WSM disease and WSS pressure. We assessed the tolerance of popular winter wheat, spring wheat, and barley cultivars in Montana to mechanical inoculation with WSMV in field studies. Winter wheat 'Brawl CL Plus' and breeding lines CO12D922 and MTV1681 demonstrated moderate WSMV incidence and minor yield penalties under WSMV inoculation, making them suitable cultivars to be grown in high-risk environments. We investigated the effects of cultivar choice, planting date, and seeding rate on grain yield and quality parameters in field studies. Our results validated current planting date recommendations for Montana. Yield reductions were observed at planting dates later than mid-September and April for winter wheat and spring wheat, respectively. No yield increase was observed when winter wheat was planted before mid-September. No meaningful and reliable economic benefits were associated with an increase in seeding rate beyond the recommended density. We developed a WSM risk prediction model and released it as the online learning tool AWaRe ('Assessment of Wheat streak mosaic Risk'). AWaRe presents the first learning tool that integrates complex information on the dynamics underlying WSM disease and relates them to the user in an interactive way. We expect the adoption of risk assessment based WSM management practices that result in a reduced economic impact through the use of this tool. The potential of different insecticides to manage WSS damage was compared to spring wheat genotypes with varying degrees of WSS resistance. Results showed that application of the systemic insecticide Thimet-20G provided effective protection of susceptible cultivar 'Reeder,' but use of solid-stem cultivars were similarly effective.
Elucidating the effect of anthropogenic land management on soil nematode community structure
(Montana State University - Bozeman, College of Agriculture, 2019) Burkhardt, Andy; Chairperson, Graduate Committee: Jamie Sherman; Shabeg S. Briar, John M. Martin, Patrick M. Carr, Jennifer Lachowiec, Cathy Zabinski, David W. Roberts, Perry Miller and Jamie Sherman were co-authors of the article, 'Perennial crop legacy effects on nematode community structure in semi-arid wheat systems' in the journal 'Applied soil ecology' which is contained within this thesis.; Shabeg S. Briar, John M. Martin, Patrick M. Carr and Jamie Sherman were co-authors of the article, 'Characterization of soil nematode community structure in semi-arid dryland barley (Hordeum vulgare L.) systems' which is contained within this thesis.
Nematodes as a taxonomic phylum are incredibly diverse and play an important role in soil biology, nutrient cycling, and soil food web function. Nematodes can be categorized into five major trophic groups including bacterivores, fungivores, herbivores, predators, and omnivores. Plant-parasitic nematodes (PPNs) affect soil food web resources through direct herbivory, while free-living (non-pathogenic) bacterivores and fungivores graze on microbes and contribute significantly to soil nutrient pools. Predatory nematodes regulate the soil food web by preying on other nematodes and invertebrates in the soil. An unbalanced soil food web community can lead to unintended impacts to other species and create a cascading effect. In agriculture, this impact can lead to low crop production and reduced revenue by means of soil ecological degradation. The goal of this project was to elucidate the nematode community structure changes under different management strategies in both agricultural and range settings. The hypotheses we tested were 1) that crop rotations eliminating fallow would positively and significantly impact the soil nematode community that would in turn self-regulate the PPN population and 2) native sagebrush steppe would have a more diverse nematode community than converted sagebrush steppe managed for livestock grazing or other uses. We did so with the following studies: 1. Quantitatively assessed nematode community structure under barley monoculture and barley-fallow vs. barley-pea rotations using multiple ecological measures and indices and correlated those measures and indices with soil chemical and physical properties as well as agronomic parameters of each system. 2. Quantitatively assessed nematode community structure under wheat-tilled fallow, wheat-no-till fallow, and no-till wheat monoculture vs. several no-till wheat-pulse rotations using multiple ecological measures and indices to evaluate long term impacts of cropping system to the nematode community. 3. Quantified taxonomic diversity and ecological indices of disturbed and undisturbed sagebrush steppe in the Bangtail Mountains west of Wilsall, Montana to evaluate disturbance regimes in a reclaimed environment.
Zinc efficiency and diversity of Montana wheat and barley
(Montana State University - Bozeman, College of Agriculture, 2017) Kaya, Eylul; Chairperson, Graduate Committee: Hikmet Budak; Levent Ozturk and Hikmet Budak were co-authors of the article, 'Micronutrient diversity of Montana wheat and barley' which is contained within this thesis.
Zn is essential for all living organisms because of its functional, structural and regulatory roles in more than 300 enzymes found in eukaryotes (McCall, 2000). In plants and humans, trace metal deficiencies cause an altered expression or function of proteins at the metabolic level and may lead to physiological drawbacks in plants and even psychological problems in humans. Plants with improved Zn status may help to alleviate these issues globally. Therefore, it is crucial to understand genes involved in Zn homeostasis. Lack of information on the micronutrient status of Montana wheat and barley was the main reason of this study and most commonly cultivated Montana wheat and barley varieties were included in the study. The aim of this study was; (I) to identify ZIP1 and IRT2 genes in Montana wheat and barley cultivars, (II) to study the physiological response, effectiveness in Zn uptake capacity and Zn translocation to plant edible parts by subjecting these cultivars to Zn deficient and Zn adequate environments and (III) to comprehend the micronutrient diversity and Zn grain localization of local wheat and barley cultivars.
Effects of a barley chromosome 6H grain protein QTL on agronomic traits, malt quality traits, and stomatal control under two irrigation and nitrogen fertilization regimes
(Montana State University - Bozeman, College of Agriculture, 2018) Mangel, Dylan J. L.; Chairperson, Graduate Committee: Andreas Fischer
Cereal grain protein concentration (GPC) is an important quality parameter, with high GPC desirable when grain is used for food or feed, while low (typically below 12- 13%) GPC is needed when barley grain is used for malting. A major QTL controlling grain protein has previously been identified on barley chromosome 6H. Based on the comparison with a co-linear region on wheat chromosome 6B, the functional status of a gene coding for a NAC transcription factor (HvNAM-1) is responsible for controlling whole-plant senescence, nutrient remobilization from leaves to developing grains, and grain protein concentration. In this context, the purpose of this study was the analysis of the influence of a low- vs. a high-grain protein allele at this locus on barley agronomic and malting quality parameters in different genetic backgrounds. Integration of the low-protein allele stably lowered GPC by 1.6-1.8%, in both years and across all combinations of genetic backgrounds and management practices. Lines with the low-protein allele matured 1.4 to 2.5 days later, dependent on management, and had stably lower malt protein and diastatic power. Effects on additional agronomic and malt quality parameters including yield, test weight, percentage of plump kernels, free amino nitrogen and alpha-amylase activity were subtler and depended on the genetic background tested. Our data also provide important information on the influence of soil N and water availability on malt quality characteristics. Overall, use of the chromosome 6H low-grain protein allele stably lowered grain and malt protein levels without important negative influences on any of the tested agronomic and malt quality parameters, indicating its usefulness in the development of new malting barley germplasm. The studied chromosome 6H GPC QTL also controls expression of a gene coding for a glycine-rich RNA-binding protein (HvGR-RBP1) that may improve drought tolerance. Stomatal conductance and canopy thermal imaging assays did not show consistent effects of the allelic state of the GPC QTL on stomatal control. However, our data showed important correlations between stomatal conductance, canopy temperature depression and agronomic parameters including yield, demonstrating the value of the performed assays for variety selection and breeding.
Genetic exploration of spike and seed morphology in a two-rowed barley nested association mapping panel
(Montana State University - Bozeman, College of Agriculture, 2018) Getz, Megan Marie; Chairperson, Graduate Committee: Jamie Sherman
Barley (Hordeum vulgare) is unique as it has six-rowed cultivars and two-rowed cultivars. The six-rowed has three fertile florets on each spikelet, while two-rowed has only a single fertile center floret per spikelet. This by itself affects seed uniformity as seed produced in the lateral florets tend to be less symmetrical and smaller in size than the center floret. Yield and plumpness are also affected by spike morphology. While the genes and alleles affecting six-rowed vs. two-rowed spikes are known, there are a number of other genes that affect additional spike morphological traits such as number of seeds per head, length of head, and compaction of spikelets. Here, a two-rowed Nested Association Mapping (NAM) population was used to genetically dissect barley spike and seed morphology. To create the population, 13 diverse founder lines of barley were crossed with Conlon, a high yielding, plump, spring variety. Approximately 80 progenies were selected from each of the Conlon by founder crosses, and then backcrossed to Conlon in hopes of exposing the advantageous traits while adapting lines to the Great Plains of the Northwest. The population varying for spike and seed morphology was grown out in a field trial in Bozeman, MT and Logan, UT where phenotypic data was collected throughout the stages of growth and harvest. At maturity (Zadok's 50) stage five heads from each of the lines were collected. Digital Image Analysis was used to measure spike length, kernel count, density, and seed size. Genetic maps were created for each family as well as a consensus map for the whole population. Associations between the phenotypic data and the genotypic data observed in the individual families and consensus map allowed us to identify QTLs conserved across multiple families as well as unique to individual families. Evidence of pleiotropic effects between traits was observed. Some of the QTLs previously were identified, and some are novel. One of the families was of particular interest due to unique QTLs impacting seeds per spike and seed weight. Additionally, several novel QTLs were identified on chromosome 7H that highly impact seed traits.
An assessment of nematodes affecting wheat in Montana
(Montana State University - Bozeman, College of Agriculture, 2018) Al-Khafaji, Riyadh Talib; Chairperson, Graduate Committee: Alan T. Dyer
Nematodes represent a major biological constraint on wheat and barley production worldwide, and yet no comprehensive assessment of plant parasitic nematodes associated with cereals has been conducted for Montana. To address this shortcoming, a survey was conducted to determine the species of plant parasitic nematodes associated with small grains, and an assessment of variation in virulence across 4 crops and 8 resistant wheat lines was conducted for Pratylenchus neglectus populations collected from across Montana. The survey, conducted across 11 counties, and found widespread distribution of P. neglectus, Tylenchorhynchus spp., and Tylenchus spp. within the state. Populations of P. neglectus were generally low (268 to 363 nematodes/kg of dry soil for 2015 and 2016, respectively). However, destructive populations were detected in 9 fields in both 2015 and 2016. In addition, populations of the cereal cyst nematode Heterodera avenae were detected. Cereal cyst nematode Heterodera filipjevi, a regulated pest, was detected in only one field. Additional species of parasitic nematode were detected, but rare. To assess the applicability of resistant crops and wheat lines for management of P. neglectus, greenhouse trials were conducted using nematode populations from within the state. In two trials conducted with resistant crops, significant interaction was detected between crops and populations of nematodes (ANOVA P< 0.001 and P= 0.01). In the first trial, populations from 3 counties were virulent on barley (mean reproductive factor = 10.9). Populations from other counties were either non-virulent on barley, or their inoculations were ineffective. In the second trial, 2 of the 3 populations were again virulent on barley (mean Rf = 4.4 and Rf = 10.7). Trials examining virulence across resistant wheat lines found no interactions between populations and wheat lines (ANOVA P= 0.60 and P= 0.93). While significant variation in reactions to the resistant lines were detected, none of the lines appeared particularly resistant to Montana populations, with mean Rf values of 13.1 and 15.4 for trials 1 and trials 2, respectively. Results suggest plant parasitic nematodes are localized problems, with P. neglectus and Heterodera species of particular concern, and that "resistant" wheat lines and barley may ineffective in managing P. neglectus in some regions of the state.

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